Variant report

Variant	nsv963581
Chromosome Location	chr3:139998123-140007344
allele	n/a
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:140004703..140007058-chr3:140009329..140011674,2	MCF-7	breast:

Extended variants
information (count: 328 )
Associated
traits (count: 53 )

Variant overlapped rSNPs/rCNVs (count:328 , 50 per page) page: 1 2 3 4 5 6 7

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	rs4076964	chr3:139998140-139998141	Weak transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
2	rs557049210	chr3:139998143-139998144	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
3	rs60794672	chr3:139998170-139998171	Weak transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
4	rs56162195	chr3:139998214-139998215	Weak transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
5	rs149715216	chr3:139998218-139998219	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
6	rs557361658	chr3:139998285-139998286	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
7	rs577328555	chr3:139998361-139998362	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
8	rs368062102	chr3:139998366-139998367	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
9	rs145549233	chr3:139998430-139998431	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
10	rs148856885	chr3:139998436-139998437	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
11	rs553803653	chr3:139998451-139998452	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
12	rs114939850	chr3:139998483-139998484	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
13	rs544363415	chr3:139998489-139998490	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
14	rs115920471	chr3:139998529-139998530	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
15	rs546105342	chr3:139998542-139998543	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
16	rs370762484	chr3:139998586-139998587	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
17	rs116267234	chr3:139998609-139998610	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
18	rs559419210	chr3:139998623-139998624	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
19	rs560322412	chr3:139998834-139998835	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
20	rs527968678	chr3:139998889-139998890	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
21	rs74549404	chr3:139998897-139998898	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
22	rs571134683	chr3:139998900-139998901	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
23	rs142539741	chr3:139998901-139998902	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
24	rs531481832	chr3:139998902-139998903	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
25	rs550322203	chr3:139998956-139998957	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
26	rs528288242	chr3:139999025-139999026	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
27	rs182481689	chr3:139999079-139999080	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
28	rs541699365	chr3:139999099-139999100	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
29	rs7620671	chr3:139999106-139999107	Weak transcription	n/a	n/a	LD-proxies of rSNP Overlapped rCNV	n/a
30	rs150934163	chr3:139999142-139999143	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
31	rs561783758	chr3:139999146-139999147	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
32	rs114100813	chr3:139999147-139999148	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
33	rs187105154	chr3:139999266-139999267	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
34	rs558844115	chr3:139999307-139999308	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
35	rs147125702	chr3:139999308-139999309	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
36	rs367838384	chr3:139999311-139999312	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
37	rs530477721	chr3:139999344-139999345	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
38	rs138524661	chr3:139999347-139999348	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
39	rs142569396	chr3:139999356-139999357	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
40	rs371253726	chr3:139999357-139999358	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
41	rs374584145	chr3:139999365-139999366	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
42	rs192076649	chr3:139999387-139999388	Weak transcription	n/a	n/a	Overlapped CNVs	n/a
43	rs527908995	chr3:139999405-139999406	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
44	rs546164825	chr3:139999420-139999421	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
45	rs570097469	chr3:139999441-139999442	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
46	rs150249228	chr3:139999491-139999492	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
47	rs547345089	chr3:139999524-139999525	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
48	rs76528304	chr3:139999531-139999532	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
49	rs562355084	chr3:139999581-139999582	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a
50	rs532791876	chr3:139999592-139999593	Enhancers Weak transcription	n/a	n/a	Overlapped CNVs	n/a

Variant related diseases (count:53)

Disease	PMID	Source
Basal cell lymphoma	17053054	CNVD
Esophageal cancer	21851588	CNVD
Uveal melanoma	21693616	CNVD
Glioblastoma multiforme	21080181	CNVD
Retinoblastoma	21504564	CNVD
Medulloblastoma	21979893	CNVD
Thoracic aortic aneurysm	21092924	CNVD
Intellectual disability	22102821	CNVD
Autism	22495311	CNVD
Lung cancer	18438408	CNVD
Cancer	21129771	CNVD
Congenital diaphragmatic hernia	21085971	CNVD
Cervical cancer	21062161	CNVD
Squamous cell cancer	20885788	CNVD
Melanoma	18172304	CNVD
T-cell prolymphocytic leukemia	19278963	CNVD
Bipolar disorder	18458673	CNVD
Breast cancer	22032731	CNVD
Breast cancer	16461572	CNVD
Neuroblastoma	17533364	CNVD
Cervical Cancer	21857958	CNVD
Melanoma	21693616	CNVD
Lung cancer	21426551	CNVD
Cancer	21637783	CNVD
Cervical cancer	21063398	CNVD
Esophageal squamous carcinoma	21637470	CNVD
Liposarcoma	21253554	CNVD
Oral cancer	21386901	CNVD
Renal cell carcinoma	19461508	CNVD
Cancer	22065749	CNVD
Endometrial cancer	22040021	CNVD
Breast cancer	21264507	CNVD
Chronic lymphocytic leukemia	21546498	CNVD
microdeletion syndrome	22180640	CNVD
T-cell prolymphocytic leukemia	17713554	CNVD
Multiple myeloma	17550852	CNVD
Basal cell lymphoma	21115979	CNVD
Ovarian cancer	22174824	CNVD
Colorectal cancer	18645599	CNVD
head and neck squamous cell carcinoma	17671120	CNVD
High-grade prostatic intraepithelial neoplasia	16573809	CNVD
Hepatocellular carcinoma	16750200	CNVD
Lung cancer	16740712	CNVD
Esophageal squamous carcinoma	18350619	CNVD
Myelodysplastic syndrome	21251322	CNVD
Blepharophimosis-ptosis-epicanthus inversus syndrome	22067867	CNVD
small cell lung cancer	20016488	CNVD
Acute lymphoblastic leukemia	21339820	CNVD
Myelofibrosis	22110671	CNVD
abnormal development	18461090	CNVD
Ependymoma	20639864	CNVD
Dyslexia	22102821	CNVD
Autism	19246517	CNVD

Chromatin state (count:59 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:139980200-139999400	Weak transcription	Pancreas	Pancrea
2	chr3:139995400-140007400	Weak transcription	HSMMtube	muscle
3	chr3:139996000-140003400	Weak transcription	H9 Cell Line	embryonic stem cell
4	chr3:139999400-139999600	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
5	chr3:139999400-139999600	Enhancers	Pancreas	Pancrea
6	chr3:139999600-140015600	Weak transcription	Pancreas	Pancrea
7	chr3:140001600-140002600	Enhancers	Psoas Muscle	Psoas
8	chr3:140002200-140002400	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
9	chr3:140002400-140003800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
10	chr3:140002600-140003000	Weak transcription	Psoas Muscle	Psoas
11	chr3:140003200-140003800	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
12	chr3:140003200-140003800	Enhancers	iPS-20b Cell Line	embryonic stem cell
13	chr3:140003200-140004200	Enhancers	HUES6 Cell Line	embryonic stem cell
14	chr3:140003200-140004400	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
15	chr3:140003200-140004600	Enhancers	iPS-18 Cell Line	embryonic stem cell
16	chr3:140003200-140004800	Enhancers	H1 Cell Line	embryonic stem cell
17	chr3:140003400-140003600	Enhancers	ES-I3 Cell Line	embryonic stem cell
18	chr3:140003400-140003800	Enhancers	HUES64 Cell Line	embryonic stem cell
19	chr3:140003400-140004000	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
20	chr3:140003400-140004000	Enhancers	iPS-15b Cell Line	embryonic stem cell
21	chr3:140003400-140004600	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
22	chr3:140003400-140004800	Enhancers	H9 Cell Line	embryonic stem cell
23	chr3:140003600-140004000	Enhancers	ES-WA7 Cell Line	embryonic stem cell
24	chr3:140003600-140004600	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
25	chr3:140003600-140009400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
26	chr3:140003800-140004400	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
27	chr3:140003800-140004400	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
28	chr3:140003800-140007400	Weak transcription	HUES64 Cell Line	embryonic stem cell
29	chr3:140004000-140007200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
30	chr3:140004200-140004400	Enhancers	Ovary	ovary
31	chr3:140004200-140004600	Weak transcription	HUES6 Cell Line	embryonic stem cell
32	chr3:140004200-140005000	Enhancers	Skeletal Muscle Female	skeletal muscle
33	chr3:140004200-140005200	Enhancers	Skeletal Muscle Male	skeletal muscle
34	chr3:140004400-140005000	Weak transcription	Ovary	ovary
35	chr3:140004400-140005600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
36	chr3:140004400-140009200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
37	chr3:140004400-140015600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
38	chr3:140004600-140004800	Enhancers	HUES6 Cell Line	embryonic stem cell
39	chr3:140004600-140005000	Enhancers	Fetal Muscle Leg	muscle
40	chr3:140004600-140005000	Enhancers	Psoas Muscle	Psoas
41	chr3:140004600-140008800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
42	chr3:140004800-140008800	Weak transcription	HUES6 Cell Line	embryonic stem cell
43	chr3:140004800-140009200	Weak transcription	H9 Cell Line	embryonic stem cell
44	chr3:140004800-140015600	Weak transcription	H1 Cell Line	embryonic stem cell
45	chr3:140005000-140005800	Enhancers	Ovary	ovary
46	chr3:140005000-140007800	Weak transcription	Skeletal Muscle Female	skeletal muscle
47	chr3:140005600-140005800	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
48	chr3:140006600-140010600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
49	chr3:140006800-140013400	Enhancers	HMEC	breast
50	chr3:140007000-140010600	Enhancers	NHEK	skin

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